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Into causing error line 130 of main.nf #61

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aboyd003 opened this issue Apr 30, 2022 · 2 comments
Open

Into causing error line 130 of main.nf #61

aboyd003 opened this issue Apr 30, 2022 · 2 comments

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@aboyd003
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Operator into has been deprecated -- it's not available in DSL2 syntax

-- Check script '/rhome/aboyd003/.nextflow/assets/nf-core/cageseq/main.nf' at line: 130

@aboyd003
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aboyd003 commented May 1, 2022

More details in case they are helpful.

N E X T F L O W ~ version 22.04.0
Run using singularity on hpcc cluster
Error details from log file:
Apr-30 16:54:21.810 [main] ERROR nextflow.cli.Launcher - @unknown
groovy.lang.DeprecationException: Operator into has been deprecated -- it's not available in DSL2 syntax
at nextflow.extension.OpCall.checkDeprecation(OpCall.groovy:333)
at nextflow.extension.OpCall.invoke1(OpCall.groovy:319)
at nextflow.extension.OpCall.invoke0(OpCall.groovy:306)
at nextflow.extension.OpCall.invoke(OpCall.groovy:166)
at nextflow.extension.OpCall.call(OpCall.groovy:113)
at nextflow.extension.ChannelExtensionDelegate.invokeExtensionMethod(ChannelExtensionDelegate.groovy:144)
at groovy.runtime.metaclass.NextflowDelegatingMetaClass.invokeMethod(NextflowDelegatingMetaClass.java:60)
at org.codehaus.groovy.runtime.callsite.PojoMetaClassSite.call(PojoMetaClassSite.java:44)
at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:47)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:125)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:139)
at Script_733b14b3.runScript(Script_733b14b3:130)
at nextflow.script.BaseScript.runDsl2(BaseScript.groovy:170)
at nextflow.script.BaseScript.run(BaseScript.groovy:203)
at nextflow.script.ScriptParser.runScript(ScriptParser.groovy:220)
at nextflow.script.ScriptRunner.run(ScriptRunner.groovy:212)
at nextflow.script.ScriptRunner.execute(ScriptRunner.groovy:120)
at nextflow.cli.CmdRun.run(CmdRun.groovy:334)
at nextflow.cli.Launcher.run(Launcher.groovy:480)
at nextflow.cli.Launcher.main(Launcher.groovy:639)

@mashehu
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mashehu commented May 1, 2022

You can either run it with an extra -dsl1 option or use the dev version (with -r dev) which is written in DSL2.

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